Description

Call variants from a BAM file using iVar

Input

name:type
description
pattern

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

bam:file

A sorted (with samtools sort) and trimmed (with iVar trim) bam file

*.bam

fasta:file

The reference sequence used for mapping and generating the BAM file

*.fa

fai:file

The index for the reference sequence used for mapping and generating the BAM file

*.fai

gff:file

A GFF file in the GFF3 format can be supplied to specify coordinates of open reading frames (ORFs). In absence of GFF file, amino acid translation will not be done.

save_mpileup:boolean

Save mpileup file generated by ivar variants

Output

name:type
description
pattern

tsv

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

*.tsv:file

iVar generated TSV file with the variants

*.tsv

mpileup

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

*.mpileup:file

mpileup output from samtools mpileup [OPTIONAL]

*.mpileup

versions

versions.yml:file

File containing software versions

versions.yml

Tools

ivar
GPL-3.0-or-later

iVar - a computational package that contains functions broadly useful for viral amplicon-based sequencing.